Background Pulmonary embolism (PE) has been cited as the most common preventable cause of death in hospitalized patients. The objectives of this study were to determine recent trends in clinical outcomes and resource utilization for hospitalized patients with a clinically recognized episode of acute PE. Methods Patients discharged from United States acute care hospitals with a primary or secondary diagnosis of PE were identified from the Nationwide Inpatient Sample during the 8-year period between 1998 and 2005. Major clinical outcomes assessed included hospital mortality and length of hospitalization. To assess resource utilization for the treatment of PE, average hospital charges for these admissions were assessed, normalized to 2005 United States dollars and adjusted to reflect the United States Consumer Price Index. Results Between 1998 and 2005, the number of hospitalized patients with a primary or secondary discharge diagnosis of PE increased from 126,546 to 229,637; hospital case-fatality rates for these patients decreased from 12.3% to 8.2% (p < 0.001); length of hospital stay decreased from 9.4 days to 8.6 days (p < 0.001); and total hospital charges increased from $25,293 to $43,740 (p < 0.001). Conclusions Between 1998 and 2005, significant improvements were observed in outcomes for patients hospitalized with clinically recognized PE, including decreases in mortality and length of hospital stay. Charges for this hospital care increased during this time period.